Mammalians have two major types of sensory neurons in the retina: rods, specialized for vision in dim-light, and cones for vision in well-lit conditions and the perception of color. Most mammals have two cone types, namely S- and M-cones. They diverge in their sensitivity to different wavelengths of light, based on their expression of different light-sensitive proteins: S-opsin for blue light and M-opsin for green light. The purpose of this project is to identify genetic differences in cones and, more specifically, to find molecules that are involved in cone synapse formation. Until now, cones have been classified mostly by the opsin they express. Recent findings in our laboratory point to the existence of additional genetic differences. Normally, the dendrites of the S-cone bipolar cell (SCBC), an interneuron that relays cone-signals to downstream neurons, exclusively contact S-cones. However, genetic disruption of the normal S- and M-opsin expression pattern in different knockout mice fails to alter that specific connection. Can we identify genes other than the opsins that are uniquely expressed in each cone type? And, can we identify molecules that facilitate the formation of the specific S-cone/SCBC synapse? To identify such molecular signatures, we have turned to single cell RNA-seq to obtain complete genetic profiles of S- and M-cones. For this study, we used the 13-lined ground squirrel that, in contrast to mouse, is diurnal and has a cone-dominated retina. The two cone types are morphologically indistinguishable, so we developed a protocol to dissociate and label live cells with an antibody targeting the extracellular domain of S-cones We then manually collected single cells for next-generation sequencing. The analysis reveals differentially expressed genes that define cone identity beyond their expression of S- or M-opsins. To validate these candidate genes for further investigation, we used similar genetic profiling technique to acquire transcriptome of different type of cones from zebrafish retinas that contain cones expressing fluorescent markers. This approach will allow a comparison of the ground squirrel and zebrafish cone transcriptome. The easy genetic manipulation using CRISPR/cas9 technique in zebrafish will facilitate the functional study of genes of interest. In addition, we also explored the function of RPE65 in cone visual function using the cone dominant ground squirrel model showing a role for continuous RPE65 activity in mammalian cone pigment regeneration.